X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyseqscommand.cpp;h=a20a383b6125e135fc1aefeec47e2bc6b892f1e9;hb=80c3fe03a8fd1635d3ad7918ff00beb973449f50;hp=e5c04949905d7edd6ba5ec45f4fd5a8214053471;hpb=8130ff9b30d872c578963f8d6f24af821b1ec33c;p=mothur.git

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index e5c0494..a20a383 100644
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -107,7 +107,17 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 					#endif
 					
 					ifstream in;
-					ableToOpen = openInputFile(fastaFileNames[i], in);
+					ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
+				
+					//if you can't open it, try default location
+					if (ableToOpen == 1) {
+						if (m->getDefaultPath() != "") { //default path is set
+							string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
+							m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+							ableToOpen = openInputFile(tryPath, in, "noerror");
+							fastaFileNames[i] = tryPath;
+						}
+					}
 					in.close();
 					
 					#ifdef USE_MPI	
@@ -122,7 +132,7 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 					#endif
 					
 					if (ableToOpen == 1) { 
-						m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine(); 
+						m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
 						//erase from file list
 						fastaFileNames.erase(fastaFileNames.begin()+i);
 						i--;
@@ -168,7 +178,17 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 					#endif
 
 					ifstream in;
-					ableToOpen = openInputFile(namefileNames[i], in);
+					ableToOpen = openInputFile(namefileNames[i], in, "noerror");
+				
+					//if you can't open it, try default location
+					if (ableToOpen == 1) {
+						if (m->getDefaultPath() != "") { //default path is set
+							string tryPath = m->getDefaultPath() + getSimpleName(namefileNames[i]);
+							m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+							ableToOpen = openInputFile(tryPath, in, "noerror");
+							namefileNames[i] = tryPath;
+						}
+					}
 					in.close();
 					
 					#ifdef USE_MPI	
@@ -181,8 +201,14 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 						}
 						
 					#endif
-					if (ableToOpen == 1) {  m->mothurOut("Unable to match name file with fasta file."); m->mothurOutEndLine(); abort = true;	}
 					
+					if (ableToOpen == 1) { 
+						m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();  abort = true;
+						//erase from file list
+						namefileNames.erase(namefileNames.begin()+i);
+						i--;
+					}
+
 				}
 			}
 
@@ -213,7 +239,17 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 					#endif
 
 					ifstream in;
-					ableToOpen = openInputFile(groupfileNames[i], in);
+					ableToOpen = openInputFile(groupfileNames[i], in, "noerror");
+				
+					//if you can't open it, try default location
+					if (ableToOpen == 1) {
+						if (m->getDefaultPath() != "") { //default path is set
+							string tryPath = m->getDefaultPath() + getSimpleName(groupfileNames[i]);
+							m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+							ableToOpen = openInputFile(tryPath, in, "noerror");
+							groupfileNames[i] = tryPath;
+						}
+					}
 					in.close();
 					
 					#ifdef USE_MPI	
@@ -226,8 +262,13 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 						}
 						
 					#endif
-					if (ableToOpen == 1) {  m->mothurOut("Unable to match group file with fasta file, not using " + groupfileNames[i] + "."); m->mothurOutEndLine(); groupfileNames[i] = "";	}
 					
+					if (ableToOpen == 1) { 
+						m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); groupfileNames[i] = "";
+						//erase from file list
+						groupfileNames.erase(groupfileNames.begin()+i);
+						i--;
+					}
 				}
 			}
 
@@ -470,7 +511,7 @@ int ClassifySeqsCommand::execute(){
 			if(processors == 1){
 				ifstream inFASTA;
 				openInputFile(fastaFileNames[s], inFASTA);
-				numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+				getNumSeqs(inFASTA, numFastaSeqs);
 				inFASTA.close();
 				
 				lines.push_back(new linePair(0, numFastaSeqs));
@@ -478,7 +519,7 @@ int ClassifySeqsCommand::execute(){
 				driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
 			}
 			else{
-				vector<int> positions;
+				vector<unsigned long int> positions;
 				processIDS.resize(0);
 				
 				ifstream inFASTA;
@@ -488,7 +529,7 @@ int ClassifySeqsCommand::execute(){
 				while(!inFASTA.eof()){
 					input = getline(inFASTA);
 					if (input.length() != 0) {
-						if(input[0] == '>'){	int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);	}
+						if(input[0] == '>'){	unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);	}
 					}
 				}
 				inFASTA.close();
@@ -496,9 +537,9 @@ int ClassifySeqsCommand::execute(){
 				numFastaSeqs = positions.size();
 				
 				int numSeqsPerProcessor = numFastaSeqs / processors;
-				
+	
 				for (int i = 0; i < processors; i++) {
-					int startPos = positions[ i * numSeqsPerProcessor ];
+					unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
 					if(i == processors - 1){
 						numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 					}
@@ -520,7 +561,7 @@ int ClassifySeqsCommand::execute(){
 	#else
 			ifstream inFASTA;
 			openInputFile(fastaFileNames[s], inFASTA);
-			numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+			getNumSeqs(inFASTA, numFastaSeqs);
 			inFASTA.close();
 			
 			lines.push_back(new linePair(0, numFastaSeqs));
@@ -761,9 +802,9 @@ int ClassifySeqsCommand::driver(linePair* line, string taxFName, string tempTFNa
 
 		for(int i=0;i<line->numSeqs;i++){
 			if (m->control_pressed) { return 0; }
-			
-			Sequence* candidateSeq = new Sequence(inFASTA);
-			
+		
+			Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
+		
 			if (candidateSeq->getName() != "") {
 				taxonomy = classify->getTaxonomy(candidateSeq);